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- [ ] **3GEX** (3' Gene Expression libraries)
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- [ ] Library transfer table (sheet in prf)
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- [ ] Library name (see [library names formats](#library-names-formats))
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- [ ] index name (see [library Index sets](Single-Cell-Gene-Expression#gene-expression-library-index-sets))
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- [ ] index sequence (optional)
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- [ ] library type incl. chemistry version
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- [ ] **coresponding libraries (required if joined analysis if 3CS or CellPlex)**
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* organism (see [references and probe sets](References-and-Probe-sets))
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- [ ] Human
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- [ ] Mouse
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- [ ] other:
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- [ ] transgenic inserts:
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- [ ] **3CS** (3' [Feature barcoding](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis) libraries)
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- [ ] Feature Reference (required [see](#feature-reference-csv-file-example))
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- [ ] TotalSeq-B (with 3GEX)
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- [ ] TotalSeq-A (less common)
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- [ ] **CellPlex** (3’ [Cell Multiplexing](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi#cmoreference) CMOs libraries)
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- [ ] Barcode-sample assignment (required, [see](#barcode-sample-assignment))
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## Library names formats:
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* PID_SPID_SPNumber (minimum requirenment, e.g. P1234_SP123_004)
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* PID_SPID_SPNumber_LibraryType (required, e.g. P1234_SP123_004_GEX)
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* PID_SPID_SPNumber_LibraryType_LibraryName (best, e.g. P1234_SP123_004_GEX_Liver01)
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## Gene expression Library Index Sets
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* Dual Index Kit **TT**, Set A : 3' Gene Expression (3GEX)
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* Dual Index Kit **NT**, Set A : 3' Antibody Capture / Feature barcoding (3CS)
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* Dual Index Kit **NN**, Set A : 3' Cell Multiplexing (CellPlex)
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## Library types
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* **3GEX** (3' Gene Expression libraries)
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* **3CS** (3' Cell Surface Protein / Antibody Capture / Feature barcoding libraries)
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|
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* **CellPlex** (3’ Cell Multiplexing CMOs libraries)
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|
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## Feature Reference CSV file ([example](https://cf.10xgenomics.com/samples/cell-vdj/7.1.0/vdj_v1_hs_pbmc2_5gex_protein/vdj_v1_hs_pbmc2_5gex_protein_feature_ref.csv))
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|
```
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id,name,read,pattern,sequence,feature_type
|
|
|
|
CD3,CD3_TotalSeqB,R2,5PNNNNNNNNNN(BC),AACAAGACCCTTGAG,Antibody Capture
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|
|
CD4,CD4_TotalSeqB,R2,5PNNNNNNNNNN(BC),TACCCGTAATAGCGT,Antibody Capture
|
|
|
|
CD8a,CD8a_TotalSeqB,R2,5PNNNNNNNNNN(BC),ATTGGCACTCAGATG,Antibody Capture
|
|
|
|
```
|
|
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|
|
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|
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## Barcode-sample assignment
|
|
|
|
|
|
|
|
```
|
|
|
|
sample_id,cmo_ids
|
|
|
|
sample1,CMO301
|
|
|
|
sample2,CMO303
|
|
|
|
``` |
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\ No newline at end of file |
